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Fluorine in PDB 7adu: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J):
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J), PDB code: 7adu was solved by V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.32 / 2.62
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.469, 159.469, 123.499, 90, 90, 90
R / Rfree (%) 20.2 / 23.2

Other elements in 7adu:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) (pdb code 7adu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J), PDB code: 7adu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7adu

Go back to Fluorine Binding Sites List in 7adu
Fluorine binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:61.4
occ:1.00
 F10 A:R7K403 0.0 61.4 1.0
C8 A:R7K403 1.3 45.0 1.0
C3 A:R7K403 2.4 32.8 1.0
C7 A:R7K403 2.4 31.9 1.0
N11 A:R7K403 2.6 42.8 1.0
C1 A:R7K403 2.8 52.0 1.0
OE1 A:GLU221 2.9 46.2 1.0
O33 A:R7K403 2.9 63.6 1.0
C2' D:DC16 3.1 34.7 1.0
CD A:GLU221 3.3 43.2 1.0
O D:HOH201 3.3 59.6 1.0
CG A:GLU221 3.6 41.4 1.0
C4 A:R7K403 3.6 35.5 1.0
C6 A:R7K403 3.6 47.9 1.0
CB A:GLU221 3.7 38.3 1.0
CB A:PRO214 3.7 39.5 1.0
C12 A:R7K403 3.8 70.8 1.0
C15 A:R7K403 3.9 71.7 1.0
N1 D:DC16 4.0 47.1 1.0
OE2 A:GLU221 4.0 57.9 1.0
C6 D:DC16 4.0 44.7 1.0
C1' D:DC16 4.1 28.2 1.0
C3' D:DC16 4.1 45.8 1.0
MG A:MG402 4.1 45.8 1.0
C5 A:R7K403 4.1 33.9 1.0
CG A:PRO214 4.2 46.9 1.0
C14 A:R7K403 4.3 74.7 1.0
C2 D:DC16 4.5 47.9 1.0
C5 D:DC16 4.6 40.3 1.0
O3' D:DC16 4.6 56.2 1.0
F9 A:R7K403 4.8 63.0 1.0
CA A:GLU221 4.8 36.7 1.0
O13 A:R7K403 4.8 77.1 1.0
O5' D:DA17 4.9 63.2 1.0
O2 D:DC16 5.0 44.2 1.0

Fluorine binding site 2 out of 2 in 7adu

Go back to Fluorine Binding Sites List in 7adu
Fluorine binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:63.0
occ:1.00
 F9 A:R7K403 0.0 63.0 1.0
C6 A:R7K403 1.4 47.9 1.0
C5 A:R7K403 2.4 33.9 1.0
C7 A:R7K403 2.4 31.9 1.0
N1 C:DG4 3.0 49.2 1.0
C6 C:DG4 3.1 42.7 1.0
O6 C:DG4 3.4 49.6 1.0
N4 D:DC16 3.4 50.6 1.0
CG A:GLN215 3.5 50.1 0.6
CG A:GLN215 3.5 50.4 0.4
C4 D:DC16 3.6 43.4 1.0
N3 D:DC16 3.6 48.4 1.0
C2 C:DG4 3.6 43.7 1.0
C4 A:R7K403 3.6 35.5 1.0
C8 A:R7K403 3.7 45.0 1.0
C5 C:DG4 3.8 39.2 1.0
CD A:GLN215 3.9 44.5 0.6
OE1 A:GLN215 3.9 40.0 0.6
CA A:GLN215 4.0 39.1 0.6
CA A:GLN215 4.0 40.9 0.4
N A:GLN215 4.1 43.7 1.0
C3 A:R7K403 4.1 32.8 1.0
N2 C:DG4 4.2 44.8 1.0
C4 C:DG4 4.2 46.8 1.0
N3 C:DG4 4.2 46.4 1.0
CB A:GLN215 4.3 41.7 0.6
CB A:GLN215 4.3 40.1 0.4
C2 D:DC16 4.4 47.9 1.0
C5 D:DC16 4.4 40.3 1.0
C A:PRO214 4.5 44.7 1.0
N7 C:DG4 4.6 44.4 1.0
CD A:GLN215 4.7 54.3 0.4
O A:PRO214 4.7 43.3 1.0
CG A:PRO214 4.8 46.9 1.0
F10 A:R7K403 4.8 61.4 1.0
NE2 A:GLN215 4.8 43.7 0.4
NE2 A:GLN215 4.8 47.6 0.6
O C:HOH216 4.8 61.8 1.0
CB A:PRO214 4.9 39.5 1.0
O2 D:DC16 4.9 44.2 1.0

Reference:

S.J.Smith, X.Z.Zhao, D.O.Passos, V.E.Pye, P.Cherepanov, D.Lyumkis, T.R.Burke Jr., S.H.Hughes. Hiv-1 Integrase Inhibitors with Modifications That Affect Their Potencies Against Drug Resistant Integrase Mutants. Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
PubMed: 33686850
DOI: 10.1021/ACSINFECDIS.0C00819
Page generated: Tue Jul 15 18:32:26 2025

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